tbuckley/cabot-search huggingface dataset:
Objective wearable measures correlate with self-reported chronic pain levels in people with spinal cord stimulation systems
Authors: Denis G. Patterson, Derron Wilson, Michael A. Fishman, Gregory Moore, Ioannis Skaribas, Robert Heros, Soroush Dehghan, Erika Ross, Anahita Kyani
Journal: npj Digital Medicine (2023)

Spinal Cord Stimulation (SCS) is a well-established therapy for treating chronic pain. However, perceived treatment response to SCS therapy may vary among people with chronic pain due to diverse needs and backgrounds. Patient Reported Outcomes (PROs) from standard survey questions do not provide the full picture of what has happened to a patient since their last visit, and digital PROs require patients to visit an app or otherwise regularly engage with software. This study aims to assess the feasibility of using digital biomarkers collected from wearables during SCS treatment to predict pain and PRO outcomes. Twenty participants with chronic pain were recruited and implanted with SCS. During the six months of the study, activity and physiological metrics were collected and data from 15 participants was used to develop a machine learning pipeline to objectively predict pain levels and categories of PRO measures. The model reached an accuracy of 0.768 ± 0.012 in predicting the pain intensity of mild, moderate, and severe. Feature importance analysis showed that digital biomarkers from the smartwatch such as heart rate, heart rate variability, step count, and stand time can contribute to modeling different aspects of pain. The results of the study suggest that wearable biomarkers can be used to predict therapy outcomes in people with chronic pain, enabling continuous, real-time monitoring of patients during the use of implanted therapies.
m6A-regulated tumor glycolysis: new advances in epigenetics and metabolism
Authors: Shi-Wei Yue, Hai-Ling Liu, Hong-Fei Su, Chu Luo, Hui-Fang Liang, Bi-Xiang Zhang, Wei Zhang
Journal: Molecular Cancer (2023)

Abstract Glycolytic reprogramming is one of the most important features of cancer and plays an integral role in the progression of cancer. In cancer cells, changes in glucose metabolism meet the needs of self-proliferation, angiogenesis and lymphangiogenesis, metastasis, and also affect the immune escape, prognosis evaluation and therapeutic effect of cancer. The n6-methyladenosine (m6A) modification of RNA is widespread in eukaryotic cells. Dynamic and reversible m6A modifications are widely involved in the regulation of cancer stem cell renewal and differentiation, tumor therapy resistance, tumor microenvironment, tumor immune escape, and tumor metabolism. Lately, more and more evidences show that m6A modification can affect the glycolysis process of tumors in a variety of ways to regulate the biological behavior of tumors. In this review, we discussed the role of glycolysis in tumor genesis and development, and elaborated in detail the profound impact of m6A modification on different tumor by regulating glycolysis. We believe that m6A modified glycolysis has great significance and potential for tumor treatment.
Unleashing T cell anti-tumor immunity: new potential for 5-Nonloxytryptamine as an agent mediating MHC-I upregulation in tumors
Authors: Paweł Stachura, Wei Liu, Haifeng C. Xu, Agnès Wlodarczyk, Olivia Stencel, Piyush Pandey, Melina Vogt, Sanil Bhatia, Daniel Picard, Marc Remke, Karl S. Lang, Dieter Häussinger, Bernhard Homey, Philipp A. Lang, Arndt Borkhardt, Aleksandra A. Pandyra
Journal: Molecular Cancer (2023)

New therapies are urgently needed in melanoma, particularly in late-stage patients not responsive to immunotherapies and kinase inhibitors. To uncover novel potentiators of T cell anti-tumor immunity, we carried out an ex vivo pharmacological screen and identified 5-Nonyloxytryptamine (5-NL), a serotonin agonist, as increasing the ability of T cells to target tumor cells.The pharmacological screen utilized lymphocytic choriomeningitis virus (LCMV)-primed splenic T cells and melanoma B16.F10 cells expressing the LCMV gp33 CTL epitope. In vivo tumor growth in C57BL/6 J and NSG mice, in vivo antibody depletion, flow cytometry, immunoblot, CRISPR/Cas9 knockout, histological and RNA-Seq analyses were used to decipher 5-NL's immunomodulatory effects in vitro and in vivo.5-NL delayed tumor growth in vivo and the phenotype was dependent on the hosts' immune system, specifically CD8+ T cells. 5-NL's pro-immune effects were not directly consequential to T cells. Rather, 5-NL upregulated antigen presenting machinery in melanoma and other tumor cells in vitro and in vivo without increasing PD-L1 expression. Mechanistic studies indicated that 5-NL's induced MHC-I expression was inhibited by pharmacologically preventing cAMP Response Element-Binding Protein (CREB) phosphorylation. Importantly, 5-NL combined with anti-PD1 therapy showed significant improvement when compared to single anti-PD-1 treatment.This study demonstrates novel therapeutic opportunities for augmenting immune responses in poorly immunogenic tumors.
Abstract B023: Using hypoxia to improve tumor infiltrating lymphocytes therapy in different subtypes of renal cell carcinoma
Authors: Marine Potez, Mohammed Alkhouli, Johannes Ali, Michael Carter, Matthew Beatty, Shari Pilon-Thomas, Jad Chahoud
Journal: Cancer Research (2023)

Abstract BACKGROUND: Improving the long-term efficacy for advanced renal cell carcinoma (RCC) remains challenging after progression on first line therapy. Adoptive cell therapy (ACT) using tumor infiltrating lymphocytes (TIL) is a promising personalized immunotherapeutic approach to treating solid tumors. Previously, TIL therapy for clear cell RCC patients showed moderate success but did not account for the distinct immune microenvironments in different subtypes of RCC such as clear cell (ccRCC), papillary (pRCC) or unclassified (uRCC) known to have different response to immunotherapy. In addition, hypoxia plays a critical role in tumor progression and therapy resistance in RCC. Therefore, the aim of this study was to evaluate TIL expansion from different subtypes of RCC under varying oxygen concentrations. METHODS: Tumor types collected from 48 patients included ccRCC (81.25%), pRCC (16.7%) and uRCC (8.3%). Tumors were minced into fragments and cultured for 4 weeks in media supplemented with high dose IL-2 (6000 IU/mL). At the end of the 4 weeks, TIL were further expanded using a rapid expansion protocol (REP) in either 20% or 5% oxygen. TIL expansion, reactivity to autologous tumor, and phenotype were evaluated in pre-REP and post-REP samples. RESULTS: Among the ccRCC, 91.7% of the samples expanded, while 100% of the pRCC and uRCC expanded. pRCC expanded more TIL than ccRCC (1.05e8 vs 6.7e7 total TIL expanded, respectively) while uRCC expanded less than the other subtypes (2.03e7). Pre-REP reactivity against autologous tumors was high for all the subtypes (88.3%, 75% and 100% for ccRCC, pRCC and uRCC respectively). The T-cell phenotype across subtypes showed a tendency of more CD4+ T-cells and less CD8+ T-cells for pRCC and uRCC, compared to ccRCC. All subtypes that underwent REP were able to expand in both 20% and 5% O2 (hypoxia) conditions. TIL expanded in hypoxia had a significantly higher percentage of tissue resident memory T-cells (CD69+CD103+; 15.1%, p&amp;lt;0.0001) when compared to the pre-REP TIL population (2%) or TIL expanded at 20% O2 (3.1%). CONCLUSION: These results demonstrate the feasibility of expanding tumor-reactive TIL from different subtypes of RCC for the first time, and highlight the advantage of exposing TIL to hypoxic conditions to enhance the differentiation of resident memory T-cells in TIL products. Citation Format: Marine Potez, Mohammed Alkhouli, Johannes Ali, Michael Carter, Matthew Beatty, Shari Pilon-Thomas, Jad Chahoud. Using hypoxia to improve tumor infiltrating lymphocytes therapy in different subtypes of renal cell carcinoma [abstract]. In: Proceedings of the AACR Special Conference: Advances in Kidney Cancer Research; 2023 Jun 24-27; Austin, Texas. Philadelphia (PA): AACR; Cancer Res 2023;83(16 Suppl):Abstract nr B023.
Abstract PR006: STING is a vulnerability in RCC independent of its innate immunity function
Authors: Pengda Liu, Zhichuan Zhu
Journal: Cancer Research (2023)

Abstract STING is an innate immune sensor for immune surveillance of viral/bacterial infection and maintenance of an immune-friendly microenvironment to prevent tumorigenesis. However, if and how STING exerts innate immunity-independent function remains elusive. Recently, we find STING expression is increased in renal cell carcinoma (RCC) patients and governs tumor growth through non-canonical innate immune signaling involving mitochondrial ROS maintenance and calcium homeostasis. We identify mitochondrial voltage dependent anion channel VDAC2 as a new STING binding partner. STING depletion potentiates VDAC2/GRP75-mediated MERC (mitochondria-ER contact) formation to increase mitochondrial ROS/calcium levels, impairs mitochondria function and suppresses mTORC1/S6K signaling leading to RCC growth retardation. STING interaction with VDAC2 occurs through STING-C88/C91 palmitoylation and inhibiting STING palmitoyl-transferases ZDHHCs by 2-BP significantly impedes RCC cell growth alone or in combination with sorafenib. Together, our studies reveal an innate immunity-independent function of STING in regulating mitochondrial function and growth in RCC, providing a rationale to target the STING/VDAC2 interaction in treating RCC. Citation Format: Pengda Liu, Zhichuan Zhu. STING is a vulnerability in RCC independent of its innate immunity function [abstract]. In: Proceedings of the AACR Special Conference: Advances in Kidney Cancer Research; 2023 Jun 24-27; Austin, Texas. Philadelphia (PA): AACR; Cancer Res 2023;83(16 Suppl):Abstract nr PR006.
Abstract IA019: Metabolic adaptations in renal cell carcinoma
Authors: W. Kimryn Rathmell
Journal: Cancer Research (2023)

Abstract Clear cell renal cell carcinoma (ccRCC) is characterized by deregulated hypoxic signaling, metabolic defects, and a complex tumor microenvironment (TME) highly enriched in both lymphoid and myeloid immune subsets. Loss of the oxygen sensing gene, von Hippel Lindau (VHL), is a critical early event in ccRCC pathogenesis and promotes stabilization of hypoxia inducible (transcription) factors (HIF) that upregulate pro-growth signaling pathways, including angiogenesis and aerobic glycolysis. However, whether Vhl loss in cancer cells impacts the frequency, energetic requirements, or other functional properties of immune subsets in the TME remains unclear. Here, using Vhl WT and Vhl KO in vivo murine kidney cancer models, we found that Vhl KO tumors across multiple clones were slower growing and promoted increased immune cell infiltration in the TME. Enhanced proinflammatory signatures in tumor associated macrophage (TAM) subsets from Vhl deficient tumors were also observed, and these features were rescued when Vhl was reintroduced to the cancer cells. Moreover, in vivo quantification of the PET tracer and glucose analog, [18F]fluorodeoxyglucose (FDG), revealed that both myeloid derived suppressor cells (MDSC) and TAM populations from Vhl KO tumors consume more glucose than myeloid subsets from Vhl intact tumors. Notably, Vhl loss did not confer increased glucose uptake in cancer cells or lymphoid subsets in vivo. Overall, these data are consistent with enhanced metabolism and proinflammatory properties observed in the myeloid compartment of human ccRCC and highlight cancer cell intrinsic mechanisms driving environmental reprograming as a means of shaping the immune landscape in ccRCC. Citation Format: W. Kimryn Rathmell. Metabolic adaptations in renal cell carcinoma [abstract]. In: Proceedings of the AACR Special Conference: Advances in Kidney Cancer Research; 2023 Jun 24-27; Austin, Texas. Philadelphia (PA): AACR; Cancer Res 2023;83(16 Suppl):Abstract nr IA019.
Abstract IA013: A zebrafish model for VHL and hypoxia signaling
Authors: Ellen van Rooijien, Stefan Schulte-Merker, Ive Logister, Emile Voest, Rachel Giles
Journal: Cancer Research (2023)

Abstract he von Hippel-Lindau (VHL) tumor suppressor gene encodes an adaptor protein that regulates an array of transcription-dependent and -independent cellular and physiological processes. Mutations in this gene cause VHL disease, congenital polycythemia, renal cell carcinoma (RCC), and several other sporadic tumor types. Although different animal models for VHL disease have been adapted, the zebrafish VHL model offers distinct opportunities. Zebrafish vhl mutants develop key aspects of the human disease condition, including activation of the hypoxia-inducible factor (HIF) signaling pathway, polycythemia, excessive neovascularization, macular edema, and pronephric abnormalities resembling early stages of RCC. The zebrafish vhl model offers a platform for the identification of genetic pathways, modifiers, and interactors involved in the development of VHL-associated neoplasms. Vhl mutants represent a unique and clinically relevant in vivo model for studying genotype-phenotype correlations and the identification of prognostic biomarkers. The amenability of zebrafish for chemical genetic screens will not only be helpful to identify novel therapeutic agents but may also reveal novel processes that require regulation by VHL. Citation Format: Ellen van Rooijien, Stefan Schulte-Merker, Ive Logister, Emile Voest, Rachel Giles. A zebrafish model for VHL and hypoxia signaling [abstract]. In: Proceedings of the AACR Special Conference: Advances in Kidney Cancer Research; 2023 Jun 24-27; Austin, Texas. Philadelphia (PA): AACR; Cancer Res 2023;83(16 Suppl):Abstract nr IA013.
Abstract PR003: PBRM1-deficient PBAF complexes target aberrant genomic loci to activate NF-κB pathway in clear cell renal cell carcinoma
Authors: Xiaosai Yao, Jing Han Hong, Amrita Nargund, Michelle S.W. Ng, Bin Tean Teh
Journal: Cancer Research (2023)

Abstract PBRM1 encodes an accessory subunit of the PBAF subclass of the SWI/SNF chromatin remodeler and the inactivation of PBRM1 is the second most frequent mutational event in kidney cancer. However, the impact of PBRM1 loss on chromatin remodeling, especially pertaining to kidney tumorigenesis, has not been well examined. Here we show that in VHL-deficient renal tumors, PBRM1 deficiency results in ectopic PBAF complexes that localize to de novo genomic loci and activate the pro-tumorigenic NF-κB pathway. PBRM1-deficient PBAF complexes, despite retaining the association between SMARCA4 and ARID2, have loosely tethered BRD7. The PBAF complexes redistribute from promoter proximal regions to distal enhancers containing NF-κB motifs; subsequently, PBRM1-deficient cells display heightened NF-κB activity in multiple models and clinical samples. The ATPase function of SMARCA4 maintains chromatin occupancy of both pre-existing and newly acquired RELA specific to PBRM1 loss, and activates downstream target gene expression. Proteasome inhibitor bortezomib abrogates RELA occupancy, suppresses NF-κB activation and delays growth of PBRM1-deficient tumors. In conclusion, PBRM1 safeguards the chromatin by repressing aberrant liberation of pro-tumorigenic NF-κB target genes by residual PBRM1-deficient PBAF complexes. Citation Format: Xiaosai Yao, Jing Han Hong, Amrita Nargund, Michelle S.W. Ng, Bin Tean Teh. PBRM1-deficient PBAF complexes target aberrant genomic loci to activate NF-κB pathway in clear cell renal cell carcinoma [abstract]. In: Proceedings of the AACR Special Conference: Advances in Kidney Cancer Research; 2023 Jun 24-27; Austin, Texas. Philadelphia (PA): AACR; Cancer Res 2023;83(16 Suppl):Abstract nr PR003.
Abstract B026: Combined inhibition of mammalian target of rapamycin (mTOR) and survivin augments radiation therapy in renal cell carcinoma
Authors: Krishnendu Pal, Vijay S. Madamsetty, Hari K. Rachamala, Shamit K. Dutta, Enfeng Wang, Debabrata Mukhopadhyay
Journal: Cancer Research (2023)

Abstract Purpose: Although renal cell carcinoma (RCC) is relatively more resistant to radiation therapy (RT) compared to other cancer indications, recent advances in single-fraction and multi-fraction stereotactic ablative radiotherapy (SABR) made it possible to achieve better outcome and reduce treatment related toxicities. In addition, with studies demonstrating that certain therapeutic agents including chemotherapies can act as radiosensitizers, the idea of combining radiotherapy with those agents are being actively pursued. Among them, mammalian target of rapamycin (mTOR) inhibitor everolimus (E) and survivin inhibitor YM155 (Y) are of special interest since they target multiple RT-resistance mechanisms simultaneously. Additionally, YM155 has been shown to help in overcoming resistance to mTOR inhibitors in various cancer including RCC. Hence, the present study aims to evaluate the efficacy of a tumor-targeted liposomal formulation combining everolimus and YM155 (EY-L) in sensitizing RCC tumors towards radiation. Experimental Design: Previously we developed a tumor-targeted liposomal formulation and used it successfully to deliver multiple drugs for the treatment of RCC in both immune-deficient and immune-competent mouse models. Here we developed a similar formulation combining everolimus and YM155 (EY-L) and assessed its efficacy in RCC cell lines in vitro and in RCC tumors in vivo. We further evaluated the efficacy of EY-L in sensitizing RCC cell lines and tumors towards radiation in vitro using clonogenic assay and in vivo in RCC xenografts in immunodeficient mice and murine RCC models in immunocompetent mice. Results: EY-L (2 mg/kg E, 1.4 mg/kg Y, twice a week intravenous administration) was better than E-L or Y-L, the corresponding single drug loaded formulations in containing the primary tumor growth and improving survival in an immunocompetent syngeneic mouse model of RCC. Furthermore, EY-L leads to significantly higher sensitization of RCC cells towards radiation in vitro than E-L or Y-L. Finally, EY-L was able to sensitize RCC tumors towards radiation therapy in both RCC xenograft and murine RCC model. Conclusion: Taken together, our study demonstrated the efficacy of a strategic combination therapy in sensitizing RCC to radiation therapy using in vitro clonogenic assay and in vivo radiosensitization studies in multiple RCC tumor models. Citation Format: Krishnendu Pal, Vijay S. Madamsetty, Hari K. Rachamala, Shamit K. Dutta, Enfeng Wang, Debabrata Mukhopadhyay. Combined inhibition of mammalian target of rapamycin (mTOR) and survivin augments radiation therapy in renal cell carcinoma [abstract]. In: Proceedings of the AACR Special Conference: Advances in Kidney Cancer Research; 2023 Jun 24-27; Austin, Texas. Philadelphia (PA): AACR; Cancer Res 2023;83(16 Suppl):Abstract nr B026.
Abstract B016: SETD2 safeguards the genome against isochromosome formation
Authors: Frank M. Mason, Anteneh T. Tebeje, Emily S. Kounlavong, Rashmi Dahiya, Logan Vlach, Tiffany Guess, Ruhee Dere, Ryoma Ohi, Peter Ly, Cheryl L. Walker, W. Kimryn Rathmell
Journal: Cancer Research (2023)

Abstract This abstract is being presented as a short talk in the scientific program. A full abstract is printed in the Proffered Abstracts section (PR012) of the Conference Program/Proceedings. Citation Format: Frank M. Mason, Anteneh T. Tebeje, Emily S. Kounlavong, Rashmi Dahiya, Logan Vlach, Tiffany Guess, Ruhee Dere, Ryoma Ohi, Peter Ly, Cheryl L. Walker, W. Kimryn Rathmell. SETD2 safeguards the genome against isochromosome formation [abstract]. In: Proceedings of the AACR Special Conference: Advances in Kidney Cancer Research; 2023 Jun 24-27; Austin, Texas. Philadelphia (PA): AACR; Cancer Res 2023;83(16 Suppl):Abstract nr B016.
Abstract PR013: An integrative genomics approach converges on a critical OXPHOS program driven by MiT/TFE fusions in translocation renal cell carcinoma
Authors: Jiao Li, Danny S. Gallant, Ananthan Sadagopan, Bingchen Li, Qingru Xu, Srinivas R. Viswanathan
Journal: Cancer Research (2023)

Abstract Translocation renal cell carcinoma (tRCC) is a rare and aggressive subtype of non-clear cell renal cell carcinoma (RCC) that represents 1-5% of kidney cancer in adults. Biologically, tRCC is driven by rearrangements that involve a member of the MiT/TFE transcription factor gene family, most commonly TFE3. There are currently no molecularly-targeted therapies specific to tRCC, owing in part to an incomplete mechanistic understanding of precisely how MiT/TFE gene fusions exert their oncogenic function. In prior work, we leveraged “histologic overlap” between tRCC and other RCC subtypes to identify tRCC cases from across multiple genomic, clinical trial, and retrospective RCC datasets, with the goal of defining the molecular landscape of this disease. Here, by analyzing pathways selectively activated in tRCC relative to other RCC subtypes in this aggregate dataset, we observed that tRCCs display strong enrichment for genes involved in oxidative phosphorylation (OXPHOS), reactive oxidative species (ROS) sensing, and the response to oxidative stress mediated by the transcription factor NRF2 (nuclear factor erythroid-derived2-like 2 [NFE2L2]). We performed chromatin immunoprecipitation and sequencing (ChIP-Seq) on a panel of tRCC and clear-cell RCC (ccRCC) cell lines, using antibodies against TFE3 as well as the active enhancer mark H3K27ac. We found that tRCC cell lines display a distinctive epigenomic profile characterized by activation of a host of genes involved in driving OXPHOS as well as NRF2 signaling. We further found that TFE3 fusions and NRF2 physically interact and genomically co-localize at multiple genes critical for mediating the response to antioxidant stress, suggesting that this metabolic phenotype is transcriptionally driven by TFE3 fusions. Genome-scale CRISPR screening in tRCC cell lines subsequently revealed tRCC-selective vulnerabilities in components of the OXPHOS machinery and in the NRF2 pathway, a distinction from most other kidney cancers in which aerobic glycolysis predominates. Overall, our genomic and functional studies implicate an essential transcriptional program driven by TFE3 fusions that converges on activation of the OXPHOS and NRF2 pathways. These molecular features provide mechanistic rationale for exploring the therapeutic targeting of OXPHOS and/or redox homeostasis pathways in tRCC. Citation Format: Jiao Li, Danny S. Gallant, Ananthan Sadagopan, Bingchen Li, Qingru Xu, Srinivas R. Viswanathan. An integrative genomics approach converges on a critical OXPHOS program driven by MiT/TFE fusions in translocation renal cell carcinoma [abstract]. In: Proceedings of the AACR Special Conference: Advances in Kidney Cancer Research; 2023 Jun 24-27; Austin, Texas. Philadelphia (PA): AACR; Cancer Res 2023;83(16 Suppl):Abstract nr PR013.